CONTEXT-INDEPENDENT FUNCTION OF A CHROMATIN BOUNDARYIN VIVO

Abstract

Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. To address this question, we randomly relocated a topological boundary functionally associated with the mouse HoxD gene cluster and show that it can indeed act similarly outside its initial genomic context. In particular, the relocated DNA segment recruited the required architectural proteins and induced a significant depletion of contacts between genomic regions located across the integration site. The host chromatin landscape was re-organized, with the splitting of the TAD wherein the boundary had integrated. These results provide evidence that topological boundaries can function independently of their site of origin, under physiological conditions during mouse development

Sequential in-cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

“…In support of this view, the disruption of TAD borders was shown to lead to their loss of insulation and concurrent mis-regulation of genes due ectopic gene-enhancer interactions (Gómez-Marín et al, 2015;Ibn-Salem et al, 2017;Lupianez et al, 2015;Rodriguez-Carballo et al, 2017). In agreement, genomic rearrangements whereby TAD boundaries are placed between regulatory elements and their targets genes result in the downregulation of the target genes along with TAD reorganization (Kraft et al, 2019;Lupianez et al, 2015;Willemin et al, 2021). However, how tissue-or gene-specific contacts can be established within one TAD is still elusive, in particular how distinct sets of enhancer sequences can interact with various subsets of transcription units and not others, in different cell types, while all located in the same chromatin domain.…”

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

“…In support of this view, the disruption of TAD borders was shown to lead to their loss of insulation and concurrent misregulation of genes due ectopic gene-enhancer interactions (Gómez-Marín et al 2015;Lupiáñez et al 2015;Ibn-Salem et al 2017;Rodríguez-Carballo et al 2017). In agreement, genomic rearrangements whereby TAD boundaries are placed between regulatory elements and their targets genes result in the down-regulation of the target genes along with TAD reorganization (Lupiáñez et al 2015;Kraft et al 2019;Willemin et al 2021). However, how tissue-or gene-specific contacts can be established within one TAD is still elusive, in particular how distinct sets of enhancer sequences can interact with various subsets of transcription units and not others, in different cell types, while all located in the same chromatin domain.…”